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At least three U.S. banks have lost millions of dollars after fraudsters gained control of payment applications that control wire transfers.

The attacks, which occurred over the last three months, show that hackers are "moving deeper and deeper into the [banking] systems," Avivah Litan, a Gartner vice president who has frequent confidential discussions with banks on security issues, said Friday. "There's no doubt about it."

Hackers have long targeted individual users, compromising account logins and passwords to execute wire transfers. Money "mules" are recruited to accept the fraudulent money in their own accounts and then transfer it again, often overseas where it can be difficult to recover.

But the latest attacks appear to be much more financially damaging. Litan said she cannot identify the affected banks, and few technical details are available about how the fraudsters accessed the wire payment application, also sometimes referred to as a wire payment switch.

To draw attention away from their activities, the banks saw attackers execute distributed denial-of-service (DDoS) attacks prior to the wire transfers taking place, said Litan, who also blogged about the issue recently.

Banks are frequent targets for DDoS attacks, which aim to overwhelm web-based applications with volumes of malicious traffic intended to cause the applications to stop responding.

Wire payment applications are typically highly protected. Only a few bank employees may hold "privileged" account credentials in order to access the systems. Fraudsters may be been able to get inside the bank's network using malicious software, Litan said.

The style of attack, where hackers exploit a weakness and parlay that into wide network access, is often referred to an advanced persistent threat. Banks can help thwart the attacks by slowing down their wire transfer systems if a DDoS attack is underway, Litan said.

"If you're under attack, you lock down a little bit," Litan said. "You don't stop everything, but you make it slower."

Officials at top U.S. banks did not have an immediate comment.

In September 2012, the FBI warned that hackers were targeting financial institution employees with malicious software in order to compromise their accounts. The hackers raised wire transfer limits, initiating overseas transfers that varied between US$400,000 and $900,000.